I hadn't played toee for over a year but had the GOG files installed with the circle of eight mod. I have just tried to launch the game and my antivirus detected a threat and seemed to just delete the whole thing. I re-downloaded through GOG but now it seems like the only way to play the game is through the GOG galaxy interface and I can't figure out how to link the circle of eight mod. Anyone else experienced this?

My suggestion is following these steps:
1) Completely uninstall both the Co8 mod and the base game;
2) Download and install again the base game using either Galaxy or the offline installer;
3) Try to launch the game either using Galaxy or directly by its own executable (note that Galaxy isn't required and the game can be launched from the executable in the installation directory);
4) Once you are sure that the base game works, you can install again the Co8 mod but, when doing this, you should check your antivirus and see if it interferes somehow (consider disabling it if necessary, but be careful about that);
5) Once the Co8 mod is installed correctly, try again to launch the game either using Galaxy or directly by its own executable, again checking the behavior of your antivirus.